Jammy and some package updates for it (#356)

.github/workflows/main.yml

@@ -27,14 +27,15 @@ jobs:
         run: echo "matrix=$(ls -1 -d packages/* | grep -v gsl | tr '\n' '\0' | xargs -0 -n 1 basename | jq -Rsc '. / "\n" - [""]')" >> $GITHUB_OUTPUT
 
   test-package:
-    name: ${{ matrix.stack }}
+    name: ${{ matrix.stack }} on ${{ matrix.os }}
     needs: list-tests
     runs-on: ubuntu-latest
     strategy:
       matrix:
         stack: ${{ fromJSON(needs.list-tests.outputs.matrix) }}
+        os: [focal, jammy]
     container:
-      image: rstudio/shinyapps-package-dependencies:focal
+      image: rstudio/shinyapps-package-dependencies:${{ matrix.os }}
     steps:
       - uses: actions/checkout@v3
       - run: ./test ${{ matrix.stack }}

CHANGELOG.md

@@ -1,3 +1,16 @@
+## September 22nd 2023
+
+### Added
+ * Dockerfile and `make` / CI configurations for an Ubuntu jammy (22.04)-based environment.
+
+### UPDATED
+ * Updated packages as necessary to support jammy as a base OS.
+    * `dockxtractr` is available in jammy, but the installation currently supports .docx only, not .doc.
+
+### REMOVED
+ * `magick` no longer needs any extra packages installed to function properly.
+ * `convertGraph` was removed from CRAN and has only one archived release from 2016, so is not being supported in this repository.
+
 ## March 15th 2021
 
 ### UPDATED

CONTRIBUTING.md

@@ -10,8 +10,8 @@ Steps
 =====
 1. [Fork](https://help.github.com/articles/fork-a-repo) the repository on Github
 2. Create a named feature branch (like `add_package_x_support`)
-3. Write your change ([see next section below](https://github.com/rstudio/shinyapps-package-dependencies/blob/master/CONTRIBUTING.md#how-to-add-system-dependency-support-for-an-r-package))
-4. Write tests for your change ([see next section below](https://github.com/rstudio/shinyapps-package-dependencies/blob/master/CONTRIBUTING.md#how-to-add-system-dependency-support-for-an-r-package))
+3. Write your change ([see next section below](https://github.com/rstudio/shinyapps-package-dependencies/blob/main/CONTRIBUTING.md#how-to-add-system-dependency-support-for-an-r-package))
+4. Write tests for your change ([see next section below](https://github.com/rstudio/shinyapps-package-dependencies/blob/main/CONTRIBUTING.md#how-to-add-system-dependency-support-for-an-r-package))
 5. Run the tests, ensuring they all pass
 6. Submit a [Pull Request](https://help.github.com/articles/creating-a-pull-request) using Github
 

Dockerfile.focal

@@ -1,5 +1,4 @@
 FROM ubuntu:focal
-MAINTAINER RStudio Docker <[email protected]>
 
 # update apt & install packages
 RUN apt-get update -qq && \

Dockerfile.jammy

@@ -0,0 +1,126 @@
+FROM ubuntu:jammy
+
+# Configure apt-get to use the mirror in us-east-1 instead of the Docker default of archive.ubuntu.com
+RUN sed -i "s/archive.ubuntu.com/us-east-1.ec2.archive.ubuntu.com/g" /etc/apt/sources.list
+
+# update apt & install packages
+RUN apt-get update -qq && \
+    DEBIAN_FRONTEND=noninteractive apt-get install -y \
+    build-essential \
+    cmake \
+    curl \
+    git \
+    gnupg \
+    libboost-all-dev \
+    libcurl4-openssl-dev \
+    locales \
+    lsb-release \
+    openssh-client \
+    protobuf-compiler \
+    sudo && \
+    rm -rf /var/lib/apt/lists/*
+
+# add R apt repository
+RUN apt-key adv --keyserver keyserver.ubuntu.com --recv-keys 0x51716619e084dab9 && \
+    echo "deb http://cran.rstudio.com/bin/linux/ubuntu jammy-cran40/" >> /etc/apt/sources.list.d/cran-rstudio.list
+
+# Ensure FreeTDS is added to unixodbc upon installation
+RUN echo tdsodbc freetds/addtoodbc boolean true | debconf-set-selections
+
+# Install libraries & database related packages separately to break up the layers
+RUN apt-get update -qq && \
+    DEBIAN_FRONTEND=noninteractive apt-get install -y \
+    gdebi-core \
+    jags \
+    libaio1 \
+    libatlas3-base \
+    libcairo2 \
+    libcairo2-dev \
+    libev-dev \
+    libfftw3-dev \
+    libgdal-dev \
+    libgraphviz-dev \
+    libgsl0-dev \
+    libmagick++-dev \
+    libmysqlclient21 \
+    libmysqlclient-dev \
+    libnetcdf-dev \
+    libpcre2-dev \
+    libprocps-dev \
+    libproj-dev \
+    libprotoc-dev \
+    libquantlib0-dev \
+    libsasl2-dev \
+    libssh-dev \
+    libsqliteodbc \
+    libxml2-dev \
+    libxt-dev \
+    libxt6 \
+    odbc-postgresql \
+    tdsodbc \
+    unixodbc \
+    unixodbc-dev \
+    wget \
+    zip && \
+    rm -rf /var/lib/apt/lists/*
+
+# Install the RStudio Professional Drivers (includes mysql drivers)
+RUN wget -q https://cdn.rstudio.com/drivers/7C152C12/installer/rstudio-drivers_2023.05.0_amd64.deb && \
+    gdebi -n rstudio-drivers_2023.05.0_amd64.deb && \
+    cat /opt/rstudio-drivers/odbcinst.ini.sample >> /etc/odbcinst.ini  && \
+    rm rstudio-drivers_2023.05.0_amd64.deb
+
+# Install JDK and Cargo separately to avoid the recommended packages
+RUN apt-get update -qq && \
+    DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends openjdk-11-jdk cargo && \
+    rm -rf /var/lib/apt/lists/*
+
+RUN apt-get update -qq && \
+    DEBIAN_FRONTEND=noninteractive apt-get install -y \
+    python3-dev \
+    python3-pip \
+    python3-venv \
+    python3-virtualenv && \
+    rm -rf /var/lib/apt/lists/*
+
+# Install Julia
+RUN wget -q https://julialang-s3.julialang.org/bin/linux/x64/1.9/julia-1.9.1-linux-x86_64.tar.gz && \
+    tar -C /usr/local -zxf julia-1.9.1-linux-x86_64.tar.gz && \
+    ln -s /usr/local/julia-1.9.1/bin/julia /usr/local/bin/julia && \
+    rm julia-1.9.1-linux-x86_64.tar.gz
+
+# Install of texlive. Use --no-install-recommends to avoid installing ~750MB of documentation
+RUN apt-get update -qq && \
+    DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends \
+    texlive-full && \
+    rm -rf /var/lib/apt/lists/*
+
+
+# add in the less secure openssl config file
+# End-user applications can optionally reference this file to allow connection to less secure systems.
+# https://community.rstudio.com/t/rmysql-to-mysql-database-on-aws-ssl-connection-error-after-deploying/100676
+COPY insecure-openssl.cnf /etc/ssl/insecure-openssl.cnf
+
+RUN apt-get update -qq && \
+    DEBIAN_FRONTEND=noninteractive TZ='Etc/UTC' apt-get install tzdata && \
+    apt-get install -s r-base-core r-base-dev | sed -e "/The following additional packages will be installed/,/^\w/!d;//d" -e "s/\br-.*\b//g" | xargs apt-get install -y
+
+# set default locale
+RUN update-locale --reset LANG=C.UTF-8
+
+# set a non-default global location for Renviron.site.
+# This would typically be found at $R_HOME/etc/Renviron.site, but we'd like it not to be a layer in the per-R version images.
+# https://stat.ethz.ch/R-manual/R-devel/library/base/html/Startup.html
+ENV R_ENVIRON /etc/R/Renviron.site
+COPY Renviron.site /etc/R/Renviron.site
+
+ARG R_VERSION=4.3.1
+
+# Install R
+RUN wget -q https://cdn.rstudio.com/r/ubuntu-2204/R-${R_VERSION}-ubuntu-2204.tar.gz -O /tmp/R-${R_VERSION}.tar.gz && \
+    mkdir -p /opt/R && \
+    tar zx -C /opt/R -f /tmp/R-${R_VERSION}.tar.gz && \
+    ln -s /opt/R/${R_VERSION}/bin/R /usr/bin/R && \
+    ln -s /opt/R/${R_VERSION}/bin/Rscript /usr/bin/Rscript && \
+    ln -s /opt/R/${R_VERSION}/lib/R /usr/lib/R && \
+    rm /tmp/R-${R_VERSION}.tar.gz

Makefile

@@ -1,24 +1,25 @@
 PACKAGE_DIRS := $(wildcard packages/*)
 PACKAGES := $(notdir ${PACKAGE_DIRS})
 PACKAGE_TESTS := $(PACKAGES:%=test-%)
-R_VERSION := 4.2.2
+R_VERSION := 4.3.1
 
 # Docker image is built on Docker Hub https://hub.docker.com/repository/docker/rstudio/shinyapps-package-dependencies/
 docker-build-%:
 	docker build -t rstudio/shinyapps-package-dependencies:$* --build-arg R_VERSION=$(R_VERSION) -f Dockerfile.$* .
 
-test-xenial-%:
-	docker run --rm --name spd-xenial-$* -v $(CURDIR):/shinyapps rstudio/shinyapps-package-dependencies:xenial /shinyapps/test $*
-
-test-all-xenial:
-	docker run --rm --name spd-xenial -v $(CURDIR):/shinyapps rstudio/shinyapps-package-dependencies:xenial /shinyapps/test
-
 test-focal-%:
 	docker run --rm --name spd-focal-$* -v $(CURDIR):/shinyapps rstudio/shinyapps-package-dependencies:focal /shinyapps/test $*
 
 test-all-focal:
 	docker run --rm --name spd-focal -v $(CURDIR):/shinyapps rstudio/shinyapps-package-dependencies:focal /shinyapps/test
 
-test-all: test-all-focal test-all-xenial
+test-jammy-%:
+	docker run --rm --name spd-jammy-$* -v $(CURDIR):/shinyapps rstudio/shinyapps-package-dependencies:jammy /shinyapps/test $*
+
+test-all-jammy:
+	docker run --rm --name spd-jammy -v $(CURDIR):/shinyapps rstudio/shinyapps-package-dependencies:jammy /shinyapps/test
+
+
+test-all: test-all-focal test-all-jammy
 
-.PHONY: test-all-focal test-all-xenial
+.PHONY: test-all-focal test-all-jammy

README.md

@@ -5,7 +5,7 @@ Some R packages require other software and libraries to be installed on the host
 function. This repository is used in [shinyapps.io](https://www.shinyapps.io/) to install those dependencies if a
 user's shinyapp utilizes an R package that requires other libraries/software to be install.
 
-To contribute to this repository, read [CONTRIBUTING.md](https://github.com/rstudio/shinyapps-package-dependencies/blob/master/CONTRIBUTING.md)
+To contribute to this repository, read [CONTRIBUTING.md](https://github.com/rstudio/shinyapps-package-dependencies/blob/main/CONTRIBUTING.md)
 
 If you'd like to request the addition of support of a specific R package, [open a github issue](https://github.com/rstudio/shinyapps-package-dependencies/issues).
 

Renviron.site

@@ -0,0 +1,4 @@
+LANG=C.UTF-8
+
+# Otherwise timedatectl will get called which leads to 'no systemd' inside Docker
+TZ=UTC